Bacteria use restriction enzymes to defend against bacterial viruses called bacteriophages (or phage). When a phage infects a bacterium, it inserts its DNA into the bacterium so that it is replicated. The restriction enzyme prevents replication of the phage DNA by cutting it into many pieces. Restriction enzymes were named for their ability to restrict, or limit, the number of strains of bacteriophage that can infect bacteria.

Restriction enzymes can be isolated from bacteria and used in the laboratory to cut DNA. They are indispensable tools in recombinant DNA technology and genetic engineering. Each restriction enzyme recognizes a short, specific sequence of nucleotide bases (the four basic chemical subunits of the linear double-stranded DNA molecule--adenine, cytosine, thymine, and guanine). These stretches in the DNA are called recognition sequences and are randomly distributed throughout the DNA. Different bacterial species make restriction enzymes that recognize different nucleotide sequences.

After a restriction endonuclease recognizes a sequence, it cuts through the DNA molecule by catalyzing the hydrolysis (splitting of a chemical bond by addition of a water molecule) of the bond between adjacent nucleotides. Bacteria prevent their own DNA from being degraded in this manner by disguising their recognition sequences. Enzymes called methylases add methyl groups (--CH3) to adenine or cytosine bases within the recognition sequence, which is thus modified and protected from the endonuclease. The restriction enzyme and its corresponding methylase constitute the restriction-modification system of a bacterial species.

All restriction enzymes are different. There are three classes of restriction enzymes, designated types I, II, and III. Types I and III enzymes are similar in that both restriction and methylase activities are carried out by one large enzyme complex, in contrast to the type II system, in which the restriction enzyme is independent of its methylase. Type II restriction enzymes also differ from the other two types in that they cleave DNA at specific sites within the recognition site; the others cleave DNA randomly, sometimes hundreds of bases from the recognition sequence.

Restriction enzymes were originally discovered and characterized by the molecular biologists Werner Arber, Hamilton O. Smith, and Daniel Nathans who shared the 1978 Nobel prize in medicine. The ability of restriction enzymes to cut DNA at precise locations has permitted researchers to isolate gene-containing fragments and recombine them with other molecules of DNA. More than 2,500 type II restriction enzymes have been identified from a variety of bacterial species. These enzymes recognize about 200 distinct sequences, which are four to eight bases in length.